It includes some books set before the New Republic era, but if it helps, here's a list of what I consider to be the best and/or essential books (with a couple of comics thrown in), in chronological order:
Rogue Planet by Greg Bear (not my favorite EU novel, but it's kind of a prequel to the NJO series)
Outbound Flight by Timothy Zahn
Shatterpoint by Matthew Stover (not really
essential, but the subject plays a role later, plus it's just an awesome book)
Allegiance by Timothy Zahn
Shadows of the Empire by Steve Perry (I personally don't think it's essential, but others do, and it's a decent book)
The Truce at Bakura by Kathy Tyers (not great, but it directly follows ROTJ and has a few important character moments)
Luke Skywalker and the Shadows of Mindor by Matthew Stover
X-wing, Series One by Michael A. Stackpole
-Rogue Squadron
-Wedge's Gamble
-The Krytos Trap
-The Bacta War
X-wing, Series Two by Aaron Allston
-Wraith Squadron
-Iron Fist
-Solo Command
The Courtship of Princess Leia by Dave Wolverton
Tatooine Ghost by Troy Denning
The Thrawn Trilogy by Timothy Zahn
-Heir to the Empire
-Dark Force Rising
-The Last Command
X-wing: Isard's Revenge by Michael A. Stackpole
The Dark Empire Trilogy by Tom Veitch (comic)
-Dark Empire
-Dark Empire II
-Empire's End
The Jedi Academy Trilogy by Kevin J. Anderson
-Jedi Search
-Dark Apprentice
-Champions of the Force
I, Jedi by Michael A. Stackpole
X-wing: Starfighters of Adumar by Aaron Allston
The Corellian Trilogy by Roger MacBride Allen
-Ambush at Corellia
-Assault at Selonia
-Showdown at Centerpoint
The Hand of Thrawn Duology by Timothy Zahn
-Specter of the Past
-Vision of the Future
Survivor's Quest by Timothy Zahn
Young Jedi Knights Books 1-6 by Kevin J. Anderson and Rebecca Moesta (young adult)
-Heirs of the Force
-Shadow Academy
-The Lost Ones
-Lightsabers
-Darkest Knight
-Jedi Under Siege
The New Jedi Order by various authors
The Dark Nest Trilogy* by Troy Denning
-The Joiner King
-The Unseen Queen
-The Swarm War
Legacy of the Force* by Aaron Allston, Karen Traviss, and Troy Denning
Fate of the Jedi* by Aaron Allston, Christie Golden, and Troy Denning
Legacy by John Ostrander and Jan Duursema (comic)
*Even though I included them in my list, I personally prefer to ignore Dark Nest, Legacy of the Force, and Fate of the Jedi, and go from The New Jedi Order directly to Legacy.
Happy reading!
